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Splittail Pogonichthys macrolepidotus, an endemic cyprinid of the Sacramento-San Joaquin estuary, has been proposed for listing as threatened under the U.S. Endangered Species Act. Almost continuous low outflow conditions in the estuary from 1987 to 1994 led to reduced abundance of young splittails, but adult abundance did not decline consistently except in the downstream portion of the species' range. This range had decreased primarily as a result of historical levee and dam construction but did not appear to have changed substantially in the past 20 years. The distribution of young splittails appears to be relatively plastic on an interannual basis. Evidence of the resilience of the species was seen when high freshwater outflows in extremely wet years (such as 1982, 1983. 1986, and 1995) resulted in high numbers of young splittails. Splittail year-class strength was positively related to freshwater outflow during the spawning season. High outflow inundates the floodplain, which provides spawning, rearing, and foraging habitat. The relatively long life span, high reproductive capacity, and broad environmental tolerances of splittails are contrasted with delta smelt Hypomesus transpacifcus and longfin smelt Spirinchus thaleichthys. other native species of special concern in the system.

The Delta Smelt, an endangered fish, has suffered a long-term decline in abundance, believed to result from, in part, to changes in the pelagic food web of the upper San Francisco Estuary. To investigate the current role of food as a factor in Delta Smelt wellbeing, we developed reference criteria for gut fullness and body condition based on allometric growth. We then examined monthly diet, prey selectivity, and gut fullness of larvae and juvenile Delta Smelt collected April through September in 2005 and 2006 for evidence of feeding difficulties leading to reduced body condition. Calanoid copepods Eurytemora affinis and Pseudodiaptomus forbesi remained major food items during spring and from early summer through fall, respectively. Other much larger copepods and macroinvertebrates contributed in lesser numbers to the diet of older juvenile fish from midsummer through fall. In fall, juvenile Delta Smelt periodically relied heavily on very small prey and prey potentially associated with demersal habitat, suggesting typical pelagic food items were in short supply. We found a strong positive selection for E. affinis and P. forbesi, neutral to negative selection for evasive calanoid Sinocalanus doerrii, and neutral to negative selection for the small cyclopoid copepod Limnoithona tetraspina and copepod nauplii, which were consumed only when extremely numerous in the environment. Feeding incidence was significantly higher in 2006, but among successfully feeding fish we found no between year difference in gut fullness. However, we did detect differences in fullness across months in both years. We found no difference in body condition of Delta Smelt between years yet our sample sizes were low in September when Delta Smelt reverted to feeding on very small organisms and fullness declined, so the longer-term effect remains unknown. Our findings suggest that: Delta Smelt had difficulty obtaining prey in spring 2005 or obtaining propersized prey in fall of both years. We detected these difficulties in some regional feeding incidence and fullness indices, but not in body condition indices.

The San Francisco Estuary supports several endemic species of fish and the southernmost populations of other species. Many of these native species and populations are imperiled or have experienced recent population declines that indicate a general decline in the estuary's capacity to support pelagic fish species. We studied the distribution and abundance of one of the estuary's native species, longfin smelt Spirinchus thaleichthys, using data from three long-term aquatic sampling programs. Each of the sampling programs we studied revealed a substantial reduction in the abundance of longfin smelt. These trends support the idea that the estuary's capacity to support pelagic fish species has been significantly reduced over the past three decades. Longfin smelt in the estuary displayed consistent patterns in relative abundance and distribution during their life cycle. We also found significant, but weak, spatial autocorrelation among sampling stations. These patterns in distribution reveal differential habitat use and migratory behavior. Managers can use these insights into longfin smelt distribution patterns to improve interpretation of sampling program results.